[English] 日本語
Yorodumi
- PDB-6fmu: Thioredoxin glutathione reductase from Schistosome mansoni in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fmu
TitleThioredoxin glutathione reductase from Schistosome mansoni in complex with 2-[4-(4-amino-butyl)-piperazin-1-yl]-ethanol
ComponentsThioredoxin glutathione reductase
KeywordsFLAVOPROTEIN / Fragment / Allosteric pocket / Schistosomiasis / FAD/NAD linked reductase
Function / homology
Function and homology information


thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / protein-disulfide reductase activity / cell redox homeostasis / flavin adenine dinucleotide binding / electron transfer activity
Similarity search - Function
Thioredoxin/glutathione reductase selenoprotein / Glutaredoxin, eukaryotic/virial / Glutaredoxin active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site ...Thioredoxin/glutathione reductase selenoprotein / Glutaredoxin, eukaryotic/virial / Glutaredoxin active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / Glutaredoxin / Glutaredoxin / FAD/NAD(P)-binding domain superfamily / Thioredoxin-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-[4-(4-azanylbutyl)piperazin-1-yl]ethanol / FLAVIN-ADENINE DINUCLEOTIDE / TRIETHYLENE GLYCOL / Thioredoxin glutathione reductase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSilvestri, I. / Fata, F. / MIele, A.E. / Boumis, G. / Williams, D.L. / Angelucci, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R21AI27635-01 United States
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Fragment-Based Discovery of a Regulatory Site in Thioredoxin Glutathione Reductase Acting as "Doorstop" for NADPH Entry.
Authors: Silvestri, I. / Lyu, H. / Fata, F. / Boumis, G. / Miele, A.E. / Ardini, M. / Ippoliti, R. / Bellelli, A. / Jadhav, A. / Lea, W.A. / Simeonov, A. / Cheng, Q. / Arner, E.S.J. / Thatcher, G.R.J. ...Authors: Silvestri, I. / Lyu, H. / Fata, F. / Boumis, G. / Miele, A.E. / Ardini, M. / Ippoliti, R. / Bellelli, A. / Jadhav, A. / Lea, W.A. / Simeonov, A. / Cheng, Q. / Arner, E.S.J. / Thatcher, G.R.J. / Petukhov, P.A. / Williams, D.L. / Angelucci, F.
History
DepositionFeb 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thioredoxin glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1984
Polymers65,0611
Non-polymers1,1373
Water9,962553
1
A: Thioredoxin glutathione reductase
hetero molecules

A: Thioredoxin glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,3968
Polymers130,1222
Non-polymers2,2746
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area10850 Å2
ΔGint-63 kcal/mol
Surface area46060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.235, 102.257, 58.661
Angle α, β, γ (deg.)90.00, 112.97, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Thioredoxin glutathione reductase


Mass: 65061.145 Da / Num. of mol.: 1 / Mutation: U597C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: Smp_048430 / Production host: Escherichia coli (E. coli)
References: UniProt: G4V8J4, thioredoxin-disulfide reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-DVK / 2-[4-(4-azanylbutyl)piperazin-1-yl]ethanol


Mass: 201.309 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H23N3O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 553 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.51 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: Bis-tris 0.1M PH = 7.0; Peg 3350 20%; KI 0.2 M

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 71563 / % possible obs: 99.5 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 16.7
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 7 % / Rmerge(I) obs: 0.7 / Num. unique obs: 4144 / % possible all: 96.9

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v6o

2v6o


Resolution: 1.8→37.13 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.49
RfactorNum. reflection% reflection
Rfree0.1812 3516 4.91 %
Rwork0.1552 --
obs0.1565 71553 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→37.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4503 0 77 554 5134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014672
X-RAY DIFFRACTIONf_angle_d1.0816333
X-RAY DIFFRACTIONf_dihedral_angle_d12.7972778
X-RAY DIFFRACTIONf_chiral_restr0.059722
X-RAY DIFFRACTIONf_plane_restr0.007795
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8003-1.8250.29251200.24092659X-RAY DIFFRACTION96
1.825-1.85110.23751260.20832677X-RAY DIFFRACTION99
1.8511-1.87870.23711290.19432727X-RAY DIFFRACTION99
1.8787-1.90810.23021400.1912703X-RAY DIFFRACTION99
1.9081-1.93930.23051500.18152711X-RAY DIFFRACTION99
1.9393-1.97280.20491320.17292710X-RAY DIFFRACTION99
1.9728-2.00860.20471340.17252682X-RAY DIFFRACTION99
2.0086-2.04730.21641320.17452747X-RAY DIFFRACTION100
2.0473-2.08910.23031530.172673X-RAY DIFFRACTION99
2.0891-2.13450.18431310.16842726X-RAY DIFFRACTION99
2.1345-2.18410.19431650.1552701X-RAY DIFFRACTION100
2.1841-2.23870.19551010.16062752X-RAY DIFFRACTION100
2.2387-2.29930.18641260.15262723X-RAY DIFFRACTION100
2.2993-2.36690.19741270.15392737X-RAY DIFFRACTION100
2.3669-2.44330.17581510.14752747X-RAY DIFFRACTION100
2.4433-2.53060.20141190.14992749X-RAY DIFFRACTION100
2.5306-2.63190.17591700.15342676X-RAY DIFFRACTION100
2.6319-2.75160.18581630.1512723X-RAY DIFFRACTION100
2.7516-2.89670.16811300.15142736X-RAY DIFFRACTION100
2.8967-3.07810.18481630.15512736X-RAY DIFFRACTION100
3.0781-3.31560.18921410.15452739X-RAY DIFFRACTION100
3.3156-3.6490.16911540.14442730X-RAY DIFFRACTION100
3.649-4.17640.13781440.13522743X-RAY DIFFRACTION100
4.1764-5.25940.13771450.12892751X-RAY DIFFRACTION100
5.2594-37.13760.19691700.17242779X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.09140.0024-0.07480.0384-0.05520.0589-0.0010.0520.0772-0.21520.0874-0.14050.0068-0.02240.00040.2759-0.07370.09450.2099-0.01040.3185156.849525.635351.5854
20.0499-0.02390.00970.04280.040.0572-0.0242-0.0656-0.0781-0.05480.0306-0.0524-0.01080.03-00.16450.0015-0.00240.17550.00240.1852135.6867-9.337661.6524
30.0179-0.02120.00260.034-0.01120.0076-0.0501-0.14190.04440.0420.0629-0.15970.07520.0942-00.1929-0.0185-0.02820.2482-0.04860.2709156.52136.731270.8275
40.3084-0.05960.0080.2194-0.07320.4056-0.0374-0.11030.02550.03350.0401-0.0043-0.0393-0.0146-00.15140.018-0.00210.1473-0.01290.1284125.13253.041571.5286
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 129 )
2X-RAY DIFFRACTION2chain 'A' and (resid 130 through 218 )
3X-RAY DIFFRACTION3chain 'A' and (resid 219 through 261 )
4X-RAY DIFFRACTION4chain 'A' and (resid 262 through 593 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more